Friday, June 26, 2015

My copy of John Parrington's new book, The Deeper Genome: Why there is more to the human genome than meets the eye, is due to arrive in about three weeks. However, we already have a number of clues about what's in the book [see How the genome lost its junk according to John Parrington]. The excerpt on Amazon [How the genome lost its junk] tells us that Parrington is aware of the controversy surrounding the ENCODE project but comes down on the side of ENCODE.

That view is shared by science writer Claire Ainsworth who wrote a review in New Scientist: Its' so last century.1 Ainsworth is a freelance science writer with a Ph.D. in developmental genetics from Oxford (Oxford, UK). She is co-founder of SciConnect, a company that teaches science communication skills to scientists.

Here's what she says in her review ....

John Parrington is an associate professor in molecular and cellular pharmacology at the University of Oxford. In The Deeper Genome, he provides an elegant, accessible account of the profound and unexpected complexities of the human genome, and shows how many ideas developed in the 20th century are being overturned.

Take DNA. It's no simple linear code, but an intricately wound, 3D structure that coils and uncoils as its genes are read and spliced in myriad ways. Forget genes as discrete, protein-coding "beads on a string": only a tiny fraction of the genome codes for proteins, and anyway, no one knows exactly what a gene is any more.

A key driver of this new view is ENCODE, the Encyclopedia of DNA Elements, which is an ambitious international project to identify the functional parts of the human genome. In 2012, it revealed not only that the protein-coding elements of DNA can overlap, but that the 98 per cent of the genome that used to be labelled inactive "junk" is nothing of the sort. Some of it regulates gene activity, some churns out an array of different kinds of RNA molecules (RNAs for short), some tiny, some large, many of whose functions are hotly debated. Parrington quotes ENCODE scientist Ewan Birney as saying at the time, "It's a jungle in there. It's full of things doing stuff." And that is one of the most apt genome metaphors I've ever read.

People, including science writers, can have different opinions about the validity of the ENCODE results and whether most of our genome is junk. They can also have different opinions about whether many of the ideas developed in the 20th century are still valid. However, I think it's only fair to at least acknowledge that others may have different opinions.

Ainsworth must be aware of the controversy over ENCODE's claim that most of our genome has a function. She could have pointed out that Parrington supports the function side but many prominent scientists support the junk DNA side. She could have noted that there have been several scientific papers published since 2012 that defend the concept of junk DNA—and defend it very well.

A good science journalist can express an opinion on a scientific controversy but good science journalists are obliged to point out to their readers that this is just an opinion and there are many expert scientists who disagree.

The readers of this New Scientist book review will think that ENCODE was the last word on the debate and that's not good science reporting.

1. The title of the online version is "DNA is life's blueprint? No, there's far more to it than that."

This is ridiculous. I'm opposed to American politicians who meddle in science teaching and I'm opposed to British politicians who do the same even though I think creationism is bunk. Politicians should not be deciding what kind of science should, and should not, be taught in schools.

It's a matter of principle. It's as wrong as when American state governments banned the teaching of evolution.1

In addition, there are other reasons why this is a bad idea.

Where do you stop? Do there also need to be laws banning the teaching of astrology, climate change denial, homeopathy, and Thatcherism? Do they need laws defining the correct history of how the traitors in the Thirteen Colonies formed an alliance with the French in order to overthrow well-meaning British governments?

Why give creationists the ammunition to claim that they are being persecuted—especially when it's true?

What's wrong with showing that creationism is bad science and refuting it in the classroom? Is that forbidden? Evolution is true, it doesn't need legal protection.

Are the Brits so afraid of creationism that such a law is necessary in order to prevent creationist teachers from sneaking it into the classroom? If so, fix that problem by educating teachers.

Was this a serious enough problem to warrant giving creationism a huge publicity boost?

The government funding agreement notes that creationism "... should not be presented to pupils at the Academy as a scientific theory ..." Why not? I think that some parts of Intelligent Design Creationism really do count as valid scientific hypotheses, albeit bad ones. Why is the government taking a stand on the demarcation problem—especially an incorrect one?

1. I'm not exactly sure who made the decision in the UK. It could be the case that "government" is just a catch phrase for decisions made by a body of science teachers and science experts. Those decisions are just implemented by the "government."

I posted this photo on Facebook yesterday. It shows a large sign on the side of Princess Margaret Hospital (Toronto, Ontario, Canada) saying "WHY IS IN OUR DNA." (Click to embiggen.)

Similar signs are appearing all over Toronto, especially at bus stops and in the subway.

What the heck does it mean? The best response on Facebook was that they meant to say "Y is in our DNA" but I don't think that's what they meant. Maybe they are talking about genetic diseases? Maybe they're asking if 90% of our genome is junk? Are they questioning whether "it" is in our DNA (Why is it in our DNA?)? Are they talking about cancer? (The research wing of Princess Margaret Hospital studies cancer.)

As it turns out, none of the above. Here's the real story: Why is in Our DNA. It's straight from the The Princess Margaret Cancer Foundation press release.

As The Princess Margaret Cancer Foundation continues to raise funds for one of the top 5 cancer research centres in the world, we’re asked often: Why is The Princess Margaret a world leader? There are many reasons the centre has achieved a world-class reputation, but this spring, in our communications with donors and the public, we are focusing on one reason—our scientists and researchers never stop asking why…

Why is the body’s immune system not able to fight off all cancers?Why does cancer return in some patients?Why did a particular cancer drug work for one patient but not any of the others?Why did one patient’s tumour shrink dramatically with radiation, but another’s barely at all?

Starting in May, you’ll see on banners outside the cancer centre, the Princess Margaret Cancer Research Tower and in various media: WHY is in our DNA. This ‘Why gene’ that our team possesses in abundance has already helped to build The Princess Margaret’s rich history of discovery and innovation, ...

Now I get it. It's because scientists at PMH have a "why" gene.

I wonder what PR firm they hired and whether they thought this through? At the very least, this is a case where punctuation would help: "Why?" is in our DNA. Maybe they should have also put a disclaimer at the bottom: "But not in your DNA."

Wednesday, June 24, 2015

Intelligent Design Creationists like to pretend that their particular version of creationism is scientific. They claim they have evidence of an intelligent designer (gods), but 99% of their literature is an attack on evolution and not a defense of a new scientific theory. Those attacks take many forms but the worst ones are the attempts to smear Darwin and associate evolutionary biology with racism and the holocaust.

Of course, no one I've referred to endorses Dylann Roof's murderous rampage. I don't doubt that they are all sincerely mortified by the association, however unintended, with such unapologetic, undisguised evil.

I mention this at all not to blame them for Roof's crime, in any way, but simply to note -- because the mainstream media covers it up -- how certain ideas tend to hang together.

The racial elements in Charles Darwin's writing, the eugenicist implications, are often brushed aside as ugly but incidental, a mere byproduct of his time and place. Yet the myth of European superiority over inferior dark peoples continues to percolate in some evolutionary thinking, a century and more after the close of the Victorian era. It seems to have found an eager student in a disturbed young man named Dylann Roof.

Monday, June 22, 2015

I'm working my way through Jerry Coyne's new book. There's lots of good stuff in there but I was particularly interested in his comment about his former Ph.D. supervisor, Richard Lewontin. The issue is whether science is confined to methodological naturalism leaving religion as the only way to investigate supernatural claims.

We've been over this many times in the past few decades but it's still worth reminding people of the only rational response to such a claim. This is from pages 91 and 92 of Faith vs. Fact: Why Science and Religion Are Incompatible.

... some scientists persist in claiming, wrongly, that naturalism is a set-in-stone rule of science. One of these is my Ph.D. advisor, Richard Lewontin. In a review of Carl Sagan's wonderful book The Demon Haunted World, Lewontin tried to explain the methods of science:

It is not that the methods and institutions of science somehow compel us to accept material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door.

That quotation has been promulgated with delight by both creationists and theologians, for it seems to show the narrow-mindedness of scientists who refuse to even admit the possibility of the supernatural and immaterial. But Lewontin was mistaken. We can in principle allow a Divine Foot in the door; it's just that we've never seen the Foot. If, for example, supernatural phenomena like healing through prayer, accurate religious prophecies, and recollection of past lives surfaced with regularity and credibility, we might be forced to abandon our adherence to purely natural explanations. And in fact we've sometimes put naturalism aside by taking some of these claims seriously and trying to study them. Examples include ESP at other "paranormal phenomena" that lack any naturalistic explanation.

Sadly, arguments similar to Lewontin's—that naturalism is a unbreakable rule of science—are echoed by scientific organizations that want to avoid alienating religious people. Liberal believers can be useful allies fighting creationism, but accommodationists fear that those believers will be driven away by any claim that science can tackle the supernatural. Better to keep comity and pretend that science by definition can say nothing about the divine. This coddling of religious sentiments was demonstrated by Eugenie Scott, the former director of an otherwise admirable anti-creationist organization, the National Center for Science Education:

First, science is a limited way of knowing, in which practitioners attempt to explain the natural world using natural explanations. By definition, science cannot consider supernatural explanations: if there is an omnipotent deity, there is no way that a scientist can exclude or include it in a research design. This is especially clear in experimental research: an omnipotent deity cannot be "controlled" (as one wag commented, "you can't put God in a test tube, or keep them out of one"). So by definition, if an individual is attempting to explain some aspect of the natural world using science, he or she must act as if there were no supernatural forces operating on it. I think this methodological naturalism is well understood by evolutionists.

Note that Scott claims naturalism as part of the definition of science. But that's incorrect, for nothing in science prohibits us from considering supernatural explanations. Of course, if you define "supernatural" as "that which cannot be investigated by science," then Scott's claims become tautologically true. Otherwise, it's both glib and misleading to say that God is off-limits because he can't be "controlled" or "put in a test tube." Every study of spiritual healing or the efficacy of prayer (which, if done properly, includes controls) puts God into a test tube. It's the same for tests of non-divine supernatural phenomena like ESP, ghosts, and out-of-body experiences. If something is supposed to exist in a way that has tangible effects of the universe, it falls within the ambit of science. And supernatural beings and phenomena can have real-world effects.

Last night was my first visit to the Café Scientifique in Streetsville (Mississauga, Ontario, Canada). I had a great time discussing "Replaying the tape of life," Stephen Jay Gould, adaptationism, contingency, random genetic drift and lots of other things. This is a great group and I'll definitely be attending the next meeting.

The venue is perfect. We met in a room above a pub (The Franklin House) on the main street in Streetsville. There was plenty of good food and good beer.

Friday, June 19, 2015

I do not agree with those who dismiss Intelligent Design Creationism because it is not science. I prefer to think of it as an approach that superficially resembles the scientific approach but fails in various ways. In this sense, it's not much different from lots of other bad examples of science.

Let's look at the way Intelligent Design Creationists describe their attempt to be scientific. This is from a recent post by that well-known scientist,1 Casy Luskin, on Eovlution News & Views (sic) [Does Intelligent Design Deserve Academic Freedom?]. In that post, Luskin lists four criteria proving that ID is a genuine scientific theory.

It's the first point on the list that I want to discuss. The link takes you to a brief description of how Intelligent Design Creationism uses the scientific method to prove that gods played a role in the history of life. Here's how it works ...

There are many detailed descriptions of the battle online so I'm not going to bother with details. The French armies had to eliminate the fortified positions at Hougoumont, La Haye Sainte, and Papelotte. They succeeded at La Haye Saint and Papelotte but the British held on to Hougoumont. This is one of the decisive skirmishes of the battle. The French committed far too many troops to the attack on Hougomount and wasted far too much time.

The diagram on the left shows the situation late in the day when the Imperial Guard is attacking Wellington's center. That attack was driven back and the retreat of the elite Imperial Guard triggered a general retreat of all French forces. Wellington signaled a general advance that didn't stop until the allies reached Paris.

Note the Prussians attacking from the East (right) the French corps under Grouchy had not prevented Blücher from carrying out his promise to support Wellington. The French were doomed as long as Wellington held out until the end of the day and that's what happened.

I've been to the battlefield twice. Here's a photo from 2010 when I went with my daughter, son-in-law, and newly born granddaughter. The big hill behind them was made for tourists so they could get an overview of the battlefield from the top. Most people think it ruined the site.

There are monuments to various military leaders all over the battlefield. Most of the thousands of men who died that day have no monuments to mark where they fell. One of Ms. Sandwalk's distant cousins, Isabella Hood, was married to John Whyte of the British Dragoons. He died at Waterloo. His wife moved to Canada.

Wednesday, June 17, 2015

Watch Jeffrey Tomkins of The Institute for Creation Science teach us about the very latest (not!) research in genomics. I haven't bothered counting the errors and misrepresentations in this video. I'm pretty sure it would take me a lot longer than 17 minutes to show where he is wrong. That's the problem.

Click on the figure below the video to show the human/chimp sequence comparison for chromosome 2 (top) and chromosome 7 (bottom). Note that the red dots fluctuate between 98-99% across the entire lengths except for a few gaps and duplications. Keep your eye on the figure as you listen to Jeffrey Tomkins tell us how the real difference is 66-85%.

Also, note how this level of similarity extends all across chromosome 2 where the comparison is to two separate chimp chromosomes. Examine the figure while Tomkins explains that the chromosome fusion idea is wrong.

After the defeat at Ligny, the Prussians retreated in good order to Wavre and by Saturday, June 17th a large part of the Prussian army had reached that town.

Meanwhile, Wellington had massed his forces on the ridge south of Mont St. Jean and he was fortifying the farm at Hougoumont on his right and the village of Papelotte on his left. In addition, he placed a garrison in La Haye Sainte, a farm right in front of his center on the main road to Brussels. As usual, most of Wellington's troops were posted on the reverse slope of the ridge where they could not be easily seen by the advancing French army and they were partially protected from cannon fire.

The map on the right (above) shows the positions of the armies on each day. As you can see, the Prussians were well-positioned to come to the aid of Wellington by advancing troops from Wavre toward the battlefield at Mont St. Jean (Waterloo). Wellington and Blücher were in touch during this day of preparation and Blücher promised to attack the French right on the following day.

The map on the right (above) shows Grouchy marching off to the East but this is not accurate. Grouchy did keep in touch with the Prussians retreating down the road to Wavre and there was a battle at Wavre the next day. However, Grouchy did not press the Prussians as hard as he should have and he did nothing to prevent them from coming to the aid of Wellington the next day. All historians agree that this failure on the part of Grouchy played a major role in Napoleon's defeat. The second map is a bit better.

Napoleon joined Ney at Quatre-Bras and pursued the Anglo-Dutch army down the road to Brussels. The French were not able to bring up their forces very quickly so they were not in position to attack on the 17th.

By that evening the French had amassed 48,000 infantry, 14,000 cavalry, and 250 guns. Wellington's force consisted of 50,000 infantry, 11,000 cavalry, and 150 guns. The Prussians committed 48,000 men out of a force twice that size.

There was a heavy rain that evening. The men huddled in their tents knew that the decisive battle would be fought the next day and thousands of them would never live to see another night.

A recent article in Nature reminded me of the importance of definitions. The article discusses evolution and evolutionary algorithms in a special issue on machine learning (Eiben and Smith, 2015). I think we all know that "evolutionary" algorithms are based on natural selection and we all know that there's more to evolution than just adaptation. It's too late to change the name of these procedures in computer science but at the very least I expect computer scientists to be aware of the difference between their procedures and real evolution.

In this paper, there's a section on "how evolutionary computation compares with natural evolution." The authors consistently use "evolution" as a synonym for "selection" or "adaptation" and they seem to be unaware of any other mechanism of evolution.

In one sense, it's okay to conflate "evolution" and "adaptation" in computer science but if that error reflects and perpetuates a fundamental misunderstanding of the nature of real biological evolution then perhaps it's time to rename these algorithms "adpatation algorithms."

Tuesday, June 16, 2015

If students are going to learn critical thinking about evolution, they need to be exposed to controversial views and challenges concerning evolution, the history of life, and evolutionary theory. The Discovery Institute agrees with this strategy. It has published a handbook called The Educator's Briefing Packet that claims to outline what teachers should cover when they teach evolution.

As you might imagine, the Discovery Institute concentrates on showing that evolution is wrong rather than focusing on whether Intelligent Design Creationism is correct. That's partly because they don't want to advocate teaching Intelligent Design Creationism in schools.

They explain the strategy on page 7 ...

Teaching this subject objectively means presenting both the scientific evidence for and against neo-Darwinian evolution. This does not mean simply criticizing evolution or only presenting the case against the neo-Darwinian model. Rather, objective instruction means:

Fully teaching the evidence for neo-Darwinian evolution from the textbook.

Covering the entire required curriculum.

Helping students understand the scientific arguments in favor of neo-Darwinian evolution as well as the scientific criticisms as they are presented in the scientific literature.

This strategy implies that students are taught something called "Neo-Darwinism" in class. Here's how they define Neo-Darwinism.

Darwin argued that natural selection had the power to produce fundamentally new forms of life. Together, the ideas of universal common descent and natural selection form the core of Darwinian evolutionary theory. "Neo-Darwinian" evolution combines our knowledge of DNA and genetics to claim that mutations in DNA provide the variation upon which natural selection acts.

Right away we have a problem since many textbooks do not describe modern evolutionary theory in this manner. The handbook doesn't explain what teachers should do if they are teaching modern evolutionarytheory instead of Neo-Darwinism but I think it's pretty obvious what the Intelligent Design Creationists would recommend if they actually understood evolution. They would still recommend criticizing it.

In a real classroom run by competent teachers, the teachers would begin by pointing out that many creationist organizations have an incorrect and distorted view of evolution and they would pass out copies of the handbook. Then they would discuss why the Discovery Institute is promoting nonsense about evolution when they claim to be experts on the subject. The class could analyze the difference between the DI version of evolution that only covers natural selection and the modern view that includes random genetic drift and population genetics. This would be a highly effective way of teaching critical thinking and exposing students to one of the most common misconceptions about evolution.

In the right hands, this could lead to a discussion about why creationists seem to resist being educated about evolution even though the correct information is readily available on the internet. The class could learn about confirmation bias, begging the question, false dichotomy, and the strawman fallacy using examples from the handbook.

The Educator's Briefing Packet contains lots of other myths and misrepresentations that are commonly found in creationist literature. Debunking and correcting these examples can also be used to foster critical thinking and teach the truth about evolution. I'd like to thank the Discovery Institute for putting them all in one place. I'd love to spend a few days in a senior high school class showing the students why these are myths and/or misconceptions.

Here's the list1 ...

Genetics:Mutations Tend to Cause Harm and Do Not Build Complexity. Darwinian evolution relies on random mutations which are acted on by natural selection, a blind and unguided process that has no goals. Such a random and undirected process tends to harm organisms. They do not seem capable of improving organisms or building new complex systems.

Biochemistry:Unguided and Random Processes Cannot Produce Cellular Complexity.Cells contain incredible complexity, similar to machine technology but dwarfing anything produced by humans. Cells use circuits, miniature motors, feedback loops, encoded language, and even error-checking machinery which decodes and repairs our DNA. Many scientists have claimed that Darwinian evolution does not appear capable of building this type of integrated complexity.

Paleontology:The Fossil Record Lacks Intermediate Fossils. The fossil record’s overall pattern is one of abrupt explosions of new biological forms and possible candidates for evolutionary transitions are the exception, not the rule. For example, the Cambrian Explosion is an event in life’s history over 500 million years ago where nearly all the major body plans of animals appear in a geological instant without any apparent evolutionary precursors.

Taxonomy:Biologists Have Failed to Construct Darwin’s Tree of Life. Biologists hoped that DNA evidence would reveal a grand tree of life where all organisms are clearly related. Yet trees describing the alleged ancestral relationships between organisms based upon one gene or biological characteristic commonly conflict with trees based upon a different gene or characteristic. This implies a challenge to universal common descent, the hypothesis that all organisms share a single common ancestor.

Chemistry:The Chemical Origin of Life Remains an Unsolved Mystery. The mystery of the origin of life is unsolved, and all existing theories of chemical evolution face major problems. Basic deficiencies in chemical evolution include a lack of explanation for how a primordial soup could arise on the early earth’s hostile environment, or how the information required for life could be generated by blind chemical reactions.

In all theses cases we have situations where the Discovery Institute is challenging the views of the vast majority of scientists who have devoted careers to studying these issues. That's a good opportunity to teach students how they should go about deciding who to believe when faced with scientific questions. Should you believe doctors or movie actors when trying to decide whether to vaccinate your children? Should you believe climatologists or politicians about climate change? Should you believe evolutionary biologists or religious leaders when trying to decide if evolution is true?

However, I'm not sure if we could ever have much of a discussion about these issues because the latest "ID the Future" podcast features a discussion between Nate Herbst and Casy Luskin about students who question evolution in class. As it turns out, many of those students have bad experiences because they end up feeling stupid when they challenge science in class. Luskin and Herbst recommend that they hide their beliefs in order to avoid such embarrassment [see Listen: Good Advice for Students Learning about Evolution]. Maybe that's not always a good idea, however, because Herbst and Luskin also have some stories about how they stumped the professors and caused them to change their minds about evolution and origins.

1. I wonder who they used as an authority on evolution in order to make up these questions?

Napoleon's Army of the North had crossed the Belgian frontier and was advancing toward Brussels. Napoleon had surprised the allied armies with his rapid advance and now they choose the risky strategy of a forward concentration in the face of an enemy attack. The Prussians had an easier task since they choose to concentrate their army at Ligny covering their supply lines to the East. The forward outposts fall back to Ligny under pressure from the French right under Grouchy. [see Battle of Waterloo]

On Thursday evening Wellington attended a ball given by the Duchess of Richmond in Brussels and it wasn't until the early hours of Friday the 16th that he gave orders to concentrate the Anglo-Dutch army at Quatre-Bras. Prince Orange was ordered to hold Quatre-Bras until the rest of the army arrived.

Wellington's strategy was to stay in contact with the Prussians at Ligny where the combined armies could defeat Napoleon. Napoleon's goal was to prevent the allied armies from supporting each other and crush one of them with overwhelming superiority of numbers. As it turned out, neither strategy succeeded on Friday, June 16th.

Ney held the Anglo-Dutch troops at bay around Quatre-Bras in a tough battle with heavy losses. He eventually took the crossroads at Quatre-Bras only to be driven back when Wellington arrived with fresh troops. Meanwhile, Napoloeon attacked the Prussians at Ligny with Grouchy's corps and the reserve that had been under his personal command. The Prussians were defeated but not destroyed [Battle of Ligny].

The map (left) shows the positions on Friday evening as the Prussian center collapses. It also shows the wandering of D'Erlon's corps that never got into either battle. It it had attacked the flank of the Prussian army Napoleon might have gained a decisive victory and if it had supported Ney it could have prevented Wellington's army from using the crossroads at Quatre-Bras. [see Waterloo: Myth and Reality]

Now comes one of the decisive moments of the Waterloo campaign. Blücher's Prussians retreated in orderly fashion on Wavre where he could remain in touch with Wellington who was forced to fall back to Wavre after the position at Quatre-Bras became untenable. Grouchy was ordered to pursue Blücher and prevent the Prussians from supporting the Anglo-Dutch army. Grouchy failed to do this because his corps did not move quickly and was confused about the direction of the Prussian retreat. As we shall see, Grouchy's failure is blamed for the defeat at Waterloo two days later.

Meanwhile, Wellington was able to fall back to a defensive position at Waterloo where he waited for the French army.

"Ligny by Ernest Crofts (1875). This representation of the battle shows Napoleon surrounded by his staff surveying the battlefield while columns of infantry advance to the front. The windmill at Brye on a hill, north west from Ligny, was a good vantage point and Blücher made it his headquarters during the battle, hence in this context it is an iconic symbol of Napoleon's victory." [Battle of Ligny]

Summoned to Waterloo: Brussels, dawn of June 16, 1815 by Robert Alexander Hillingford. Officers leaving the Duchess of Richmond's ball.

Monday, June 15, 2015

Michael Behe first proposed the idea of "irreducible complexity" in Darwin's Black Box back in 1996. He defines it as ...

By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on.

That's interesting. Let's look at the paper to see what it says. The reference is Muskhelishvili, G. and Travers, A. (2015) and the relevant passage is on page 4556.

Thus, the holistic approach assumes self-referentiality (completeness of the contained information and full consistency of the different codes) as an irreducible organisational complexity of the genetic regulation system of any cell. Put another way, this implies that the structural dynamics of the chromosome must be fully convertible into its genetic expression and vice versa. Since the DNA is an essential carrier of genetic information, the fundamental question is how this self-referential organisation is encoded in the sequence of the DNA polymer.

What they are saying is that proper gene regulation requires both transcription factors AND a particular organization of the chromosome that facilitates transcription. It also requires input from metabolic pathways. If any one of these three things are missing then the cell cannot regulate gene expression in the same manner as cells where all three are present.

The authors then go on to discuss how this system could have evolved. Look at Figure 3 of their paper (below) where they clearly show the relationships between transcription, supercoiling, and small regulatory molecules. The paper describes their belief that this "irreducible organisational complexity" arose by evolution from these three existing features.

So, these authors are using "irreducible complexity" to describe a system that's clearly possible according to their understanding of evolution. Uncommon Descent states that this is exactly the same sense in which the term is used by Michael Behe. In fact, it quotes a physicist named David Snoke who says,

Three comments: 1) the authors are “serious” scientists, not fringe people. 2) They are using “irreducible complexity” in the same sense as Behe. This is not a case of accidental use of the same phrase to mean something different. Their term “holistic” is another way of saying the same thing, that the system requires all of its parts to work. 3) This “holistic” approach is one that is becoming common in systems biology. I have a paper coming out on that, in the works.

We've been telling Intelligent Design Creationists for years that irreducibly complex systems can easily arise by naturalistic processes (i.e. evolution). I'm really glad that they have finally seen the light.

That should be the end of any more posts saying that irreducibly complex systems can't evolve.

It was 200 years ago today that Napoleon's army crossed the Belgian border at Charleroi and advanced on Quatre-Bras in order to split the Prussian and British armies. By occupying the central position, Napoleon hoped to defeat each army separately and occupy Brussels and the channel ports.

Neither Blücher nor Wellington were expecting such a rapid advance so Napoleon gained the element of surprise in the opening days of the campaign [Battle of Waterloo].

The Prussian outposts were quickly overrun and the army was ordered to assemble at Ligny. Napoleon's right, under Marshal Grouchy, pursued the retreating Prussians while the left, under Marshal Ney, marched on Quatre Bras in order to prevent the British army from uniting with the Prussians.

It's particularly important to note that just presenting correct scientific facts isn't enough to correct myths and misinformation. You need to discuss the misinformation and show why it is wrong. This method is supported by numerous studies.

What it means is that if you want to correct misinformation about evolution, you have to address the false beliefs of your audience. You can't correct the beliefs of evolution deniers without bringing up the various forms of creationism and showing why they are wrong. In other words, teach the controversy.

Some of my American friends tell me that this is legally impossible in American schools. If they are right, then creationism wins. Ironically, by using the courts to keep all mention of creationism out of the public schools, these friends are playing right into the hands of the anti-evolution crowd and making it impossible to debunk their myths and misconceptions.

The meeting is on Sunday evening at 7:00 pm at The Franklin House, 263 Queen St. in Sreetsville. This is a relatively new Café Scientifique so new people are more than welcome. The talk is very informal (no slides or powerpoint) and there will be lots of time for discussion and debate. I'm told that various "refreshments" will be available to help make the evening more enjoyable.

Stephen Jay Gould wrote a book about the role of chance in evolution. He called it "Wonderful Life." On the surface it's a book about the Burgess Shale and the Cambrian explosion but there's a powerful message as well. Gould is interested in why some species survive while others go extinct. Are the survivors better adapted than the losers of is it a matter of luck? We could answer this question if we could carry out an experiment.

I call this experiment "replaying life's tape." You press the rewind button and, making sure you thoroughly erase everything that actually happens, go back to any time and place in the past—say, to the seas of the Burgess Shale. Then let the tape run again and see if the repetition looks at all like the original. If each replay strongly resembles life's actual pathway, then we must conclude that what really happened pretty much had to occur. But suppose that the experimental versions all yield sensible results strikingly different from the actual history of life? What could we then say about the predictability of self-conscious intelligence? or of mammals? or of vertebrates? or of life on land? or simply of multicellular persistence for 600 million years?
Stephen Jay Gould (1989) pp. 48-50

Friday, June 12, 2015

Here's a YouTube video of a talk by Michael Lynch from February 2015. He was talking at Darwin Week at the National Institute for Mathematical and Biological Synthesis at the University of Tennessee (USA).

The talk begins with a warning that evolution has gone beyond Darwinism. Lynch emphasizes, "Mutation, drift, and the origin of subcellular features." If you haven't been able to follow the discussion on the perils of adaptationism, then watch this lecture to get a sense of what it's all about.

I'm a big fan of Michael Lynch and I hope you will also be a fan after you learn more about his views.

Thursday, June 11, 2015

Peggy Whitson is a biochemist. She did her Ph.D. with Kathleen Mathews at Rice University in Houston, Texas, USA. I frequently refer to her work on the lac repressor and its interaction with lac operator sequences [see Repression of the lac Operon]. Here are some of her papers. Once you understand this stuff, you are in a better position to judge the ENCODE results and the role of spurious binding sites.

Hsieh, W.T., Whitson, P.A., Matthews, K.S., and Wells, R.D. (1987) Influence of sequence and distance between two operators on interaction with the lac repressor. Journal of Biological Chemistry, 262: 14583-14591.

The influence of additional operator or pseudooperator sequences on the lactose repressor-operator interaction has been investigated. Results of kinetic and equilibrium binding measurements suggest an important in vivo role for the Z-gene pseudooperator in repressor-operator binding; the formation of a ternary, looped complex is indicated by the influence of secondary operator sites on binding parameters. Although the binding affinity of the Z-gene pseudooperator [Oz] is only approximately 1/30 that observed for the primary operator [O], the binding affinity to DNA containing both Oz and O is significantly higher than either sequence alone or the sum of the two. This synergistic effect is enhanced further by replacing the pseudooperator sequence [Oz] with the primary operator sequence and results in an even stronger ternary complex in plasmids with duplicate primary sites. The distance between the center of the two primary operators affects the formation of a ternary complex in the linear DNA molecules. Decreased dissociation rate constants were observed with spacing of operator-like sequences between 300 and 500 base pairs (bp). Minimal influence of the second operator on repressor binding is observed when the operators are separated by approximately 4000 or approximately 100 bp. The significant influence of distance on kinetic and equilibrium parameters was demonstrated by measurements on plasmid pRW1511 [Oi-O-PL-Oz] cleaved with restriction enzymes either in the polylinker region to place Oi-O and Oz on opposite ends of the linear plasmid or outside this region to maintain the sites within 500 bp. These results are consistent with the formation of operator-repressor-pseudooperator ternary complex to generate a looped DNA structure.

The binding affinity of the Escherichia coli lactose repressor to operator-containing plasmids was increased by negative supercoiling of the DNA. The increased affinities observed were dependent on the sequence context of the DNA as well as the degree of supercoiling. Dissociation rate constants for plasmids containing a single operator site decreased as a function of the negative supercoil density. However, the presence of pseudooperators in the plasmid DNA in addition to the primary operator sequence resulted in a significant decrease in the operator-plasmid dissociation rate at higher negative supercoil densities. Approximately eight ionic interactions were determined for both the supercoiled plasmids and the linear DNAs examined. These results suggest that the stabilization provided by the topology of supercoiled DNA affects the nonionic component of the protein-DNA interaction. The ability to form a ternary complex of protein with two DNA segments is increased by the presence of multiple operator-like sites on the DNA. Furthermore, supercoiling DNA with multiple operator-like sequences profoundly diminishes the dissociation rate and results in a remarkably stable ternary, presumably looped complex (t1/2 approximately 28 h). These data suggest a critical role in vivo for DNA topology and pseudooperator(s) in transcriptional regulation of the lac operon.

The dissociation of the repressor-operator complex from a series of negatively supercoiled plasmid DNAs was examined as a function of the sequence context, orientation, and spacing. The plasmids were grouped into four classes, each with common sequence context. The highest dissociation rate constants were observed for the plasmids containing only a single operator (or pseudooperator) sequence, while approximately 10-fold lower rate constants were measured for plasmids with the I gene pseudooperator in conjunction with either the Z gene pseudooperator or the primary operator. Comparison of the behavior of these two classes of plasmids demonstrated the importance of two operator sequences and supported a model of DNA loop formation to stabilize the repressor-operator complex (Whitson, P. A., and Matthews, K. S. (1986) Biochemistry 25, 3845-3852; Whitson, P. A., Olson, J. S., and Matthews, K. S. (1986) Biochemistry 25, 3852-3858; Whitson, P. A., Hsieh, W. T., Wells, R. D., and Matthews, K. S. (1987) J. Biol. Chem. 262, 4943-4946; Krämer, H., Niemöller, M., Amouyal, M., Revet, B., von Wilcken-Bergmann, B., and Müller-Hill, B. (1987) EMBO J. 6, 1481-1491). The third class, with intermediate dissociation rate constants, was comprised of plasmids which contained the primary operator and the higher affinity pseudooperator normally located in the Z gene. Neither the additional presence of the I gene pseudooperator nor the orientation of the primary operator relative to the Z gene pseudooperator significantly affected the dissociation rate constants. The binding characteristics of this group of plasmids demonstrated the essential role of the Z gene pseudooperator in the formation of intramolecular ternary complex and suggested an in vivo function for this pseudooperator. Plasmids containing two primary operator sequences were the class with lowest dissociation rate constants from lac repressor, and minimal effects of salt or spacing on dissociation of this class were observed. These data are consistent with formation of an intramolecular complex with a looped DNA segment stabilized by the combination of increased local concentration of binding sites and torsional stresses on the DNA which favor binding in supercoiled DNA.

The dissociation kinetics for repressor-32P-labeled operator DNA have been examined by adding unlabeled operator DNA to trap released repressor or by adding a small volume of concentrated salt solution to shift the Kd of repressor-operator interaction. The dissociation rate constant for pLA 322-8, an operator-containing derivative of pBR 322, was 2.4 × 10-3 s-1 in 0.15 M KCl. The dissociation rate constant at 0.15 M KC1 for both Xplac and pIQ, each of which contain two pseudooperator sequences, was ~6 × l0-4 s-1. Elimination of Elimination flanking nonspecific DNA sequences by use of a 40 base pair operator-containing DNA fragment yielded a dissociation rate constant of 9.3 × 10-3 s-l. The size and salt dependences of the rate constants suggest that dissociation occurs as a multistep process. The data for all the DNAs examined are consistent with a sliding mechanism of facilitated diffusion to/from the operator site. The ability to form a ternary complex of two operators per repressor, determined by stoichiometry measurements, and the diminished dissociation rates in the presence of intramolecular nonspecific and pseudooperator DNA sites suggest the formation of an intramolecular ternary complex. The salt dependence of the dissociation rate constant for pLA 322-8 at high salt concentrations converges with that for a 40 base pair operator. The similarity in dissociation rate constants for pLA 322-8 and a 40 base pair operator fragment under these conditions indicates a common dissociation mechanism from a primary operator site on the repressor.

Saturday, June 06, 2015

There's an interesting discussion going on at Uncommon Descent. Barry Arrington is wondering who to believe when it comes to evolutionary theory and many of the ID regulars have chimed in [Authority in evolutionary theory]. Clearly, this is an important issue for them because they don't want to be accused of not understanding evolution. They want to protect their version of Darwinism.

They seemed to have reached a consensus. They say you can't be an authority on evolutionary theory unless you have published a scientific paper on the subject in the last decade or so. What this means is that they can dismiss the views of many evolution supporters because we don't meet the minimum qualification.1 Our view on what is, and isn't, proper evolutionary theory are just personal opinions so they don't count.

Unfortunately for them, this also eliminates Barry Arrington, Vincent Torley, Denyse O'Leary, Casey Luskin, Stephen Meyer, Jonathan Wells, Jonathan McLatchie, Michael Behe, Salvador Cordova, Jonathan Bartlet, Michael Egnor, Cornelius Hunter, Gordon Elliot Mullings, Ann Gauger and just about everyone else in the Intelligent Design Creationist camp. If they stick to their guns, it means that nothing posted on the ID blogs is anything more than a personal opinion by someone who is not an authority on evolutionary theory.

So, who are they going to believe now? My first thought is that this can only be good for the evolution side since people who publish scientific articles on evolutionary theory are not ID supporters. It means that the Intelligent Design Creationists are obligated to trust many prominent evolution biologists as authorities while dismissing most of their own crowd.

I don't think that's what they have in mind. What they have in mind is that people like Jim Shapiro and other critics of modern evolutionary theory are the real authorities because they have published in the scientific literature. I suppose it's part of a strategy to maintain the illusion that "Darwinism" is deeply flawed.

The one good thing that will come out of this discussion, I'm sure, is that the number of posts and comments on their blogs will be greatly reduced since the general consensus is that none of them are authorities on the subject of evolution. Lot's of people are going to have to shut up because they haven't published anything on evolutionary theory.2

Strange, but I will miss Barry Arrington and Denyse O'Leary's attacks on evolutionary theory. They will now be criticized by their own people as non-authorities whenever they post.

1. I have never published a paper in the scientific literature on evolutionary theory.

Friday, June 05, 2015

Everybody loves Vij's. We were lucky. We arrived late at 5:20 for the first sitting when the restaurant opens at 5:30. The lineup was not as big as I've seen in the past and we were able to get seated when Vij opened up.

Left to right; Gordon Moran, Me, Chris Hogue, Jerry Coyne.

We talked about computer games. travel, India, Singapore, food, science, books, religion, evolution, politics, and solved most of the problems of the world. (Beer helps.) The food was delicious. Check out the entire meal, with photos, on Jerry's blog: Noms: Vij’s Indian restaurant in Vancouver.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

Disclaimer

Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.